Biology AS notes

Biology AS notes

1. Cell Structure
Cell is the basic unit of all living organisms
Tissue is a layer or group of cells of a similar type, which together perform a particular function
Organ is a structure within a multicellular organism that is made up of different types of tissue working together to perform a particular function
System is a group of organs/ distinct structures working together to achieve a particular function
Vascular system a closed system of tubes of spaces conducting fluids. (Xylem and phloem in plants) (Blood vascular system (heart, arteries, veins and capillaries in animals)
Organelle is a functionally and structurally distinct part of a cell
Cytoplasm is the contents (protoplasm) of a cell, excluding the nucleus; consisting of the cytosol and the organelles
Cell Surface Membrane ¬is a very thin membrane (7nm) surrounding all cells; it is partially permeable and controls the exchange of materials between the cell and its environment
Nucleus is a relatively large organelle found in eukaryotic cells. The nucleus contains the cell’s DNA and therefore controls the activities of the cell
Chromatin is the loosely coiled form of chromosome during interphase of the cell cycle; chromatin is made of DNA and proteins and is visible as loosely distributed patches or fibres in the nucleus when stained
Nucleolus is visible as a densely stained body; its function is to manufacture ribosomes using information in its own DNA
Nuclear envelope is two membranes, situated closely together, that surround the nucleus; the envelope is perforated with nuclear pores
Nuclear pores control the exchange of material between the nucleus and nucleoplasm
Nucleoplasm is the contents of the nucleus
Mitochondrion is the organelle where aerobic respiration takes place
Endoplasmic Reticulum (ER) a network of flattened sacs running through the cytoplasm of eukaryotic cells; molecules (particularly proteins) can be transported through the cell inside the sacs. ER is continuous with the outer membrane of the nuclear envelope. Rough Endoplasmic Reticulum (RER) is studded with ribosomes and organises synthesis of proteins and their transport in the cell, whereas Smooth Endoplasmic Reticulum manages the synthesis of lipids and steroids.
Golgi apparatus is an organelle that consists of a stack of flattened sacs, constantly forming at one end and breaking up into Golgi vesicles at the other end; Golgi vesicles carry their contents to various parts of the cell, usually to the cell surface membrane for secretion; the Golgi apparatus collects, sorts and modifies proteins
Ribosome is a tiny organelle found in a large number of cells (70s 20nm in prokaryotes and 80s 25nm in eukaryotes). Ribosomes are made of proteins and ribosomal RNA and consists of two subunits. They are the sites of protein synthesis
Lysosome is a spherical organelle found in eukaryotic cells. It contains hydrolytic enzymes and has a variety of destructive function, such as removal of old cell organelles
Centriole is one of two small, cylindrical structures found just outside the nucleus in animal cells that help control spindle formation during nuclear division
Microtubules are tiny tubes made of proteins alpha and beta tubulin. Alpha and beta tubulin form dimers that are joined end to end to form long protofilaments. 13 such filaments line up alongside each other to form a cylinder with a hollow centre. Has 3 main functions; form cytoskeleton and provide mechanical support, form intracellular transport, and form spindle during cell division
Cell wall is a wall surrounding prokaryote, plant or fungal cells. The wall containing strengthening material that protects the cells from mechanical damage, supports it and prevents it from bursting by osmosis if the cell is surrounded by a solution with higher water potential
Plasmodesmata are pore like structures found in pant cell walls; that form a narrow thread of cytoplasm between neighbouring cells allowing the controlled passage of materials from one cell to another
Vacuole is an organelle found in eukaryotic cells. A large permanent central vacuole is a typical feature of plant cell. Has a variety of functions including; storage of biochemical such as salts, sugars and waste products. Temporary phagocytic vacuoles may also form in animal cells
Tonoplast is the partially permeable membrane that surrounds the plant vacuoles
Chloroplast is the photosynthesis organelle in eukaryotes
Chlorophyll is the green pigment responsible for light capture in algae and plants
Granum is a stack of circular thylakoids in plant
Thylakoids is a flattened, membrane-bound, fluid-filled sac, which is the site of the light-dependant reactions of photosynthesis in chloroplasts
Protoctist a member of the protoctista kingdom
Magnification = (Size of image) / (Actual size)
Prokaryotes
Average diameter: 0.5-5.0 micrometres
DNA: naked, circular, lies freely in cytoplasm
Ribosomes: 70s
Organelles: very few organelles present. No membrane bound organelles present.
Cell wall: Present consisting of either murein or peptidoglycan

Eukaryotes
Average diameter: typically 40 micrometres
DNA: contained in nucleus, linear, associated to histone proteins forming chromosomes
Ribosomes: 80s
Organelles: many types of organelles present (extensive compartmentalisation)
Cell wall: Maybe present. (Cellulose cell wall in plants, chitin cell wall in fungi)

2. Biological molecules

Macromolecule is a large biological molecule (protein, polysaccharide, nucleic acid, lipids)

Polymer is a giant molecule made from several, similar, repeating subunits of monomers (lipids are NOT polymers)

Monomer is a relatively simple molecule which is used as the basic building block for the synthesis of a polymer; many monomers are joined together to make a polymer, usually by a condensation reaction (monosaccharides, amino acids, nucleotides)

Glycosidic bond A C-O-C link between two monosaccharide molecules, formed by a condensation reaction

Amylose is a polymer of alpha glucose monomers linked by 1-4 linkages, forming a linear, curved, compact, helical chain – is a constituent of starch

Amylopectin is a polymer of alpha glucose monomers linked by both 1-4 and 1-6 linkages, forming a branched chain – is a constituent of starch

Glycogen is a polysaccharide made of alpha glucose, similar in structure to amylopectin however tend to be even more branched (have more 1-6 linkages). Glycogen granules act as glucose stores in the liver and muscles

Cellulose is a polysaccharide made up of beta glucose monomers linked by l-4 linkages. Hydrogen bonds can form between cellulose molecules. 60-70 cellulose molecules can be tightly cross-linked by hydrogen bonds to form micro fibrils are held together by further hydrogen bonding to form cellulose fibres

Triglyceride is a lipid whose molecules are made up of a glycerol and three fatty acids

Phospholipids is a substance whose molecules are made up of a glycerol, two fatty acids and a phosphate group; a bilayer of phospholipids forms the basic structure of all cell membranes

Peptide bond is a C-N link between two amino acid molecules formed by a condensation reaction

Polypeptide is a long chain of amino acids formed by condensation reactions between one or more amino acids; proteins are made up of one or more polypeptide chains

Primary structure is the sequence of amino acids in a polypeptide chain

Secondary structure is the structure of a protein molecule resulting from the regular coiling of folding of the amino acid chain

Alpha helix is the helical structure of polypeptide chain held in place by hydrogen bonding

Beta pleated sheet is the loose, sheet like structure formed by hydrogen bonding between parallel polypeptide chains

Tertiary structure the compact structure of a protein molecule resulting from the three dimensional coiling of the already folded amino acid chain due to; Hydrogen bonds, disulfide bridges, ionic bonds, and weak hydrophobic interactions

Quaternary structure the three dimensional arrangement of two or more polypeptides, or of a polypeptide and a prosthetic group (non-protein component)

Globular protein is a protein whose molecules are folded into a roughly spherical shape, which is often water soluable and metabolically active, as hydrophobic R groups point inwards maintaining the shape of the molecule, whereas hydrophilic R-groups point outwards and are on the surface of the molecule maintaining soluability (haemoglobin)

Haemoglobin the red pigment found in RBC, whose molecule contains four iron atoms within a globular protein made up of four polypeptides (two alpha globin, and two beta globin molecules), and that combines reversibly with oxygen

Fibrous protein is a protein molecule whose molecules who have a relatively long, thin structure that is generally insoluable and metabolically inactive and whose function is usually structural (keratin, collagen)

Collagen is a fibrous protein consisting of three polypeptide chains each in the shape of a helix. Three helical polypeptides are wound around each other to form a triple helix. Almost every third amino acid is glycine. Triple helix is held together by hydrogen bonds and some covalent bonds. Covalent bonds form between adjacent triple helix amino acids R-groups, forming fibrils. Staggered fibrils lie alongside each other forming fibres.

Water the god send
•	Good solvent of ions and polar molecules
•	Transport medium (in vascular systems of plants and animals)
•	High specific heat capacity  makes water resistant to temperature changes
•	High latent heat of vapourisation allowing organisms to use evaporation as cooling mechanism
•	Water is most dense at 4 degrees Celsius, so ice floats; reducing the tendency of large bodies of water to freeze completely
•	High surface tension and cohesion (important in flow of water in vascular tissue)
•	Water as a reagent important during photosynthesis and hydrolysis mechanisms

3. Enzymes

Enzyme is a globular protein molecule that acts as a biological catalyst

Active site is a cleft/depression on the outer surface of the enzyme to which the specific substrate molecule is allowed to bind

Lock and Key Hypothesis Is the idea that the enzyme has a particular shape into which the substrate fits exactly

Induced fit mechanism adds the idea that the enzyme, and substrate can change shape slightly as the substrate molecule enters the enzyme in order to ensure a perfect fit caused by interactions between R-groups at the active site and the substrate

Activation Energy is the minimum amount of energy required for particles to collide successfully in order for the reaction to proceed

Competitive inhibitor is a molecule which has a shape similar to the substrate and complementary to the active site, and so can occupy the active site and prevent the substrate from binding. This reduces the Km of a substrate but Vmax is the same

Non-competitive inhibitor is a molecule that can bind to a site on the enzyme other than the active site (allosteric site). The binding results in a distortion of enzyme shape that ripples across to the active site, and prevents substrate from binding. This reduces the Vmax but the Km of substrate remains the same.

4. Cell membranes and transport

Diffusion the net movement of molecules form a region of higher concentration to a region of lower concentration down a concentration gradient, as a result of the random movement of particles.

Facilitated diffusion is the diffusion of substance through transport proteins in a cell membrane; the proteins provide hydrophilic areas that allow molecules or ions to pass through which would otherwise be less permeable to them

Osmosis is the net movement of water molecules form a region of higher water potential to a region of lower water potential, down the water potential gradient, through a partially permeable membrane

Water potential is a measure of tendency of eater to move from one place to another

Active transport is the movement of molecule or ions through transport proteins across a cell membrane, against their concentration gradient, using energy from hydrolysis of ATP

Endocytosis is the bulk movement of substance into a cell, by the infolding of cell surface membrane to form vesicles containing the substance. It is an active process

Exocytosis is the bulk movement of substance out of a cell, by the fusion of vesicles containing the substance with the cell surface membrane. It is an active process

Phospholipids is the main constituent of the bilayer. Hydrophobic interior acts as barrier to the movement of polar substances across the cell membrane. Length and saturation of fatty acid tails determines the fluidity of the cell surface membrane. Hydrophilic phosphate heads form hydrogen bonds with the water in aqueous environment, stabilising the membrane

Cholesterol is a small molecule with a hydrophilic head and hydrophobic tail that regulates the fluidity and mechanical stability of the bilayer

Glycolipid is a phospholipid attached to a short carbohydrate chain that can act as an antigen marker or take part in cell adhesion

Glycoprotein is a membrane protein attached to a short carbohydrate chain that can act as a receptor for cell signalling or take part in cell recognition

Channel proteins transmembrane proteins that allow facilitated diffusion to occur

Carrier proteins membrane proteins that allow active transport to occur through conformational changes in shape

5. Nucleic acids and protein synthesis

Nucleotide is the basic monomer unit that make up nucleic acid polymers (DNA, RNA). Nucleotides have 3 components; a nitrogenous base, a phosphate group, and a pentose sugar.
DNA molecules are made of two polynucleotide strands lying side by side, running in opposite directions, held by hydrogen bonding between complementary purines and pyrimidines.
(Purine A pairs with pyrimidine T (or U in RNA) with 2 H bonds)
(Purine G always pairs with pyrimidine C with 3 H bonds)

DNA (Deoxyribonucleic acid) is a polynucleotide that contains the deoxyribose pentose sugar, and contains four bases; Adenine (A), Thymine (T), Guanine (G), Cytosine (C).
RNA (Ribonucleic acid) is a polynucleotide that contains the ribose pentose sugar, and contains four bases; Adenine (A), Uracil (U), Guanine (G), Cytosine (C)
Polynucleotide is the polymer resulting from the formation of phosphodiester bonds between nucleotides by condensation reaction linking the 5-carbon of one sugar and the 3-carbon of the next, and so the polynucleotide is said to have 3’ and 5’ ends
DNA replication is the process of synthesising two new molecules of DNA from a parent molecule of DNA through semi-conservative replication, in which the new molecule consists of one new strand and one strand from the parent DNA molecule

1.	DNA double helix unwinds as the hydrogen bonds between the bases break (catalyse by DNA helicase)
2.	In nucleoplasm there are free activated nucleotides
3.	Bases of activated nucleotides pair up with its complementary base on the old DNA strands
4.	DNA polymerase enzyme seals the sugar phosphate back bone by forming phosphodiester bonds between adjacent nucleotides
5.	Extra phosphates are released from activated nucleotides
6.	Two DNA molecules are formed consisting of one new strand and one parent strand

Protein synthesis is the process by which the genetic code is used to determine the sequence of amino acids in the formation of proteins. It is a two step-process comprising of transcription and translation

Transcription is the process in which genetic information on DNA is copied into an mRNA molecule

1.	DNA double helix unwinds as hydrogen bonds between bases break
2.	RNA polymerase enzyme binds to promoter region
3.	Free RNA molecules’ nitrogenous bases bind to complementary bases on DNA template strand through hydrogen bonding
4.	RNA polymerase seals sugar phosphate backbone by forming phosphodiester bonds between adjacent nucleotides
5.	RNA polymerase reaches terminator sequence and unbinds from DNA
6.	H bonds between nitrogenous bases break, mRNA forms
7.	DNA double helix reformed at end of transcription

Translation is the process in which genetic information carried on mRNA is used to synthesize polypeptide molecule

1.	mRNA molecules attach to ribosomes in cytoplasm
2.	tRNA molecule in cytoplasm have site for protein attachment on one end, and a specific anticodon on the other end
3.	tRNA carries specific amino acid to mRNA molecule
4.	anticodon of tRNA binds to specific codon on mRNA
5.	second tRNA attaches to mRNA molecule
6.	Peptide bonds formed between amino acids of adjacent tRNA molecules
7.	Peptide bond formation catalysed by enzyme peptidyl transferase

6. Mitotic cell cycle

Chromosomes is a thread like structure consisting of DNA tightly coiled around histone proteins that support its structure.

Cell cycle is the series of events that take place leading to its division and duplication into two daughter cells consisting of; interphase, nuclear division and cell division

1.	During interphase cell carries out its normal function
2.	Sell is signalled in order to replicate
3.	DNA replicates so each chromosome consists of two sister chromatids in S phase
4.	During G1 cells make RNA, enzymes and other proteins needed for growth
5.	During G2 New DNA is checked for errors, and preparations are made for replication
6.	Nucleus divides into two at M phase

Mitosis is the process by which the nucleus replicates consisting of 4 stages; Prophase, Metaphase, Anaphase, and Telophase






Prophase

1.	Chromosomes condense- chromatids coil up and become shorter and thicker
2.	Nuclear envelope breaks down
3.	Nucleolus breaks down
4.	Centrosomes replicate just before prophase and move to opposite poles of the cell to set up spindle apparatus

Metaphase

1.	Centrosomes reach poles and form spindle apparatus
2.	Chromosomes line up across equator of spindle, attached to spindle by the centromere

Anaphase

1.	Spindle fibres constrict (microtubules break down)
2.	Sister chromatids migrate to opposite poles centromere first, pulled by spindle fibres

Telophase

1.	Nucleolus begins to reform
2.	Nuclear envelope begins to reform
3.	Remains of spindle broken down
4.	Chromatids reach poles of spindle and uncoil

Cytokinesis is the division of cytoplasm and cell into two by constriction of the edges of the cell membrane

Biological significance of mitosis

1.	Growth
2.	Replacement of cells and repair of tissue
3.	Asexual reproduction (vegetative propagation)
4.	Immune response

Centromere is the constricted central region holding two sister chromatids together to which microtubules of spindle attach via kinetochore

Kinetochores are protein molecules that bind specifically to DNA at centromere and microtubules

Centrosome is an organelle that consists of a pair of centrioles surrounded by a large number of proteins that control the production of microtubules that act as MTOCs for spindle construction

Telomere is a structure that seals the ends of chromosomes in order to ensure that when DNA is replicated the ends of the molecules are included

Telomerase is the enzyme that adds extra DNA to the molecule that acts as the molecules telomere

Stem cell is an undifferentiated cell which is capable of giving rise to indefinitely more cells of the same type, and from which certain other cells arise by differentiation

Cancer is a disease caused by an uncontrolled division of abnormal cells in the body

1.	Carcinogens cause mutations in cell, transforming oncogenes
2.	Cancerous cell does not respond to growth inhibition signals so continues to divide
3.	Cancerous cells rapidly divide mitotically
4.	Cancerous cells are not removed by immune system , and take up nutrients for division
5.	Rapid mitosis takes place
6.	Tumour becomes larger, characteristics of cell become abnormal
7.	Tumour supplied with blood and lymph
8.	Tumour metastasizes, cells invade other tissue and form secondary cancers

7. Transport in plants

Transpiration is the loss of water vapour from a plant to its environment, by diffusion down a water potential gradient; most transpiration takes places though the stomata in the leave

Factors affecting transpiration:

Humidity
Air movement
Light intensity
Temperature

Parenchyma is thin walled cells used as packing tissue; forming cortex in roots and stems, modified parenchyma containing chloroplast make up leaf mesophyll.
Have many functions such as;
1.	 food storage (starch),
2.	when turgid they help support plant preventing wilting,
3.	air spaces between cells allow gas exchange

Collenchyma Is modified parenchyma with extra cellulose deposits ate corners of the cell providing extra strength. Forms midrib of leaves

Sclerenchyma fibres are long elongated cells with lignified walls that help support the plant

Mesophyll is the internal tissue of a leaf blade consisting of an upper layer of palisade mesophyll (main photosynthetic tissue) and a lower spongy mesophyll with large air spaces for gas exchange
Upper epidermis is a thin transparent layer allowing light to reach mesophyll, covered with thick waxy cuticle to prevent water loss
Lower epidermis contains stomata for gas exchange
Stoma is a pore in the epidermis of a leaf, bounded by two guard cells and is needed for efficient gas exchange
Transport of water from leaf to atmosphere
1.	Water vapour diffuses from an air space through an open stoma. Carried away from leaf surface by air movements, marinating water potential gradient
2.	Water  evaporates from mesophyll cell walls into the sub stomatal air space
3.	Water moves through mesophyll cell wall, or from cytoplasm into cell wall
4.	Water leaves a xylem vessel through a pit and enter the cytoplasm or cell wall of mesophyll cell
5.	Water moves up the xylem vessel to replace the water lost from leaf
Xylem consists primarily of xylem vessel elements and is responsible for mechanical support and transport of water and mineral ions.
Vessel elements are elongated, dead cells with an empty lumen, lignified walls, and no end walls between neighbouring vessel elements forming a long hollow continuous tube called the xylem vessel.

 Xylem vessel elements have pits not laid down with lignin that allow lateral movement of water to neighbouring cells to prevent an air lock, and allow water to reach surrounding living cells

The movement of water up through xylem vessels is by mass flow
Water molecules form hydrogen bonds with each other (cohesion)
Water molecules are also attracted to cellulose and lignin (adhesion)
Cohesive and adhesive forces allow water to move through xylem as a continuous column

Transport of water from root to stem and leaf

1.	Removal of water from xylem vessels in the leaf reduces the hydrostatic pressure
2.	Hydrostatic pressure at base of plant is high
3.	Water moves up xylem vessel in continuous channels due to difference in pressures

Root pressure is the increase in hydrostatic pressure at the base of plant, in which cells surrounding the xylem pump solutes into xylem by active transport. Decreasing the water potential in xylem causes more water to enter xylem by osmosis increasing the hydrostatic pressure
Endodermis is a one cell thick layer that surrounds vascular tissue in stems and roots
From root hair to xylem
1.	Water potential in xylem vessels is lower than in cortex cells
2.	Water can move across cortex either through the apoplast or symplast pathways
a.	Apoplast pathway is when water moves through cells along cell walls
b.	Symplast pathway is when water moves through cell through cytoplasm and the interconnecting plasmodesmata
3.	Once the water reaches the endodermis the apoplast pathway is blocked as cells in the endodermis have a thick waxy band of suberin deposited in their cell walls (Casparian  strip)
4.	Water can only move through passage cells that do not have extensive suberin depositing through symplast pathway.
5.	Once across endodermis water moves down concentration gradient through pericycle into xylem
From soil into root hair
1.	Water moves into root hairs by osmosis down a water potential gradient
2.	Cytoplasm of root hairs has large quantities of dissolved inorganic ions and organic substances to maintain the water potential gradient
Translocation is the process of transporting assimilates from the source to the sink by mass flow. A hydrostatic pressure gradient is created by the active loading of sucrose at the source, and the active unloading of sucrose at sink.
Loading sucrose into phloem
1.	Sucrose is loaded into a companion cell or directly into a sieve tube element by active transport
2.	Hydrogen ions are actively pumped out of companion cell into its cell wall adjacent to a source
3.	This creates a large excess of hydrogen ions in the apoplast pathway
4.	Hydrogen ions move back into the companion cell down the concentration gradient through co-transporter protein for hydrogen and sucrose
5.	Sucrose carried into companion cell against its concentration gradient
6.	Sucrose molecules diffuse into sieve tube element through plasmodesmatal links

Phloem primarily consists of sieve tube elements with associated companion cells, responsible for translocation of assimilates such as sucrose through a plant
Sieve tube element is a living cell that has cell wall, cell surface membrane, cytoplasm, ER and mitochondria. However; the amount of cytoplasm is very small and only forms a thin layer lining the inside of the cell wall. There is no nucleus or ribosomes. Sieve elements form sieve plates with neighbouring sieve elements
Companion cell has the ‘typical’ structure of a plant cell and is associated closely to a sieve tube element by numerous plasmodesmata
Xerophytes are plant species that have adapted to survive in extreme conditions
Main adaptations of xerophytes
1.	Thick waxy cuticle to reduce water loss
2.	Epidermal hairs to retain moisture around leaf surface
3.	Leaves reduced to spines to reduce surface area (cacti)
4.	Stomata are found in pits
8. Transport in mammals
Closed double circulatory system – Blood always remains within the blood vessels so is closed, and for one completer journey around the body the blood flows through the heart twice for the systemic circulation and the pulmonary circulation.
Artery is a blood vessel that transports blood, swiftly and at high pressures, to tissues


Arteries and Veins both have walls made up of 3 layers:
1.	An inner endothelium (squamous epithelium) which is smooth to minimise friction with moving blood
2.	A tunica media containing smooth muscle, collagen, and elastic fibres
3.	A tunica externa containing collagen and elastic fibres
Structure and function of Artery
1.	Thick tunica externa capable of withstanding high blood pressure that develop in artery
2.	Thick tunica media has large amounts of elastic fibres, that allow the artery to stretch and recoil while blood is moving at high pressures in order to maintain and even out blood flow
Arterioles forms as arteries branch and help control the volume of blood reaching into tissue
Capillaries allow exchange of substance between blood and tissues. Capillaries are made up of a single layer of endothelial cells and has an approximate diameter of 7 micrometres. Red blood cells squeeze through capillaries and a brought to close proximity with respiring cells
Veins return blood to the heart
Structure and function of Vein
1.	Veins have semi-lunar valves at regular intervals to prevent back flow of blood
2.	Pressure in the vein is produced by skeletal muscles contracting close to it
Red Blood Cells (RBC) cell containing haemoglobin pigment for transport of oxygen around the body
Structure and function of RBC
1.	RBC have a biconcave disc shape providing large surface area to volume ratio
2.	RBC are very small so can squeeze through capillaries
3.	RBC have no nucleus, no mitochondria and no ER to maximise space for haemoglobin
4.	RBC are flexible
Haemoglobin dissociation curve
The S shaped curve is caused by the effect of binding of oxygen to haemoglobin. When an oxygen molecule binds to haemoglobin, the haemoglobin molecule distorts is shape and has a greater affinity for a second oxygen molecule to bind and so on and so forth.
The Bohr shift is the movement of the oxygen dissociation curve to the right at high partial pressures of carbon dioxide. At high partial pressures of carbon dioxide oxyhaemoglobin dissociates more readily and can be explained as so:
1.	Carbon dioxide is continually reproduced by respiring cells
2.	Carbon dioxide diffuses from the cells into the cytoplasm, from where some of which diffuses into RBC
3.	In cytoplasm of RBC carbonic anhydrase enzyme rapidly catalyses reaction between carbon dioxide and oxygen forming carbonic acid
4.	Carbonic acid readily dissociates into hydrogen and bicarbonate ions
5.	Hydrogen ions have a greater affinity from oxygen causing oxyhaemoglobin
6.	Hydrogen combines with haemoglobin forming hameoglobinic acid, and oxygen is released
Acclimatisation is the process in which the body compensates for low partial pressures of oxygen at high altitudes by producing greater number of red blood cells, to increase haemoglobin concentration per unit volume of blood and volume of oxygen absorbed
The heart is the hollow muscular organ that pumps blood through the circulatory system through rhythmic contractions and dilations. The heart is made of cardiac muscle.
Aorta is the largest artery and supplies blood to systemic circulation from heart
Pulmonary artery supplies deoxygenated blood to pulmonary circulation
Venae cava return deoxygenated blood from systemic circulation to heart
Pulmonary vein returns oxygenated blood from pulmonary circulation
Coronary arteries are on the surface of the heart providing oxygenated blood to cardiac tissue
Septum acts as a wall separating the left side of the wall from the right side
The upper chamber in the heart are the atria and the lower chambers are the ventricles
The left atrium and left ventricle are separated by the Bicuspid valve (atrioventricular valve)
The right atrium and right ventricle are separated by the Tricuspid valve (atrioventricular valve)
Cardiac cycle is the sequence of events that occur as the heart beats
Control of the heart beat
1.	Each cardiac cycle begins at the right atrium at the sinoatrial node (SAN) which is myogenic
2.	As the muscle in the SAN contracts it produces an electrical excitation wave which sweeps through all of the muscles in the atria of the heart. This excitation wave causes the atria to contract (atrial systole)
3.	The excitation wave reaches another patch of cells at the base of the right atrium  called the atrioventricular node (AVN)
4.	The AVN delays the impulse for a fraction of a second before it travels down into the ventricles (this ensures ventricles contract after atria)
5.	The excitation wave moves swiftly down through the septum, along purkyne tissue
6.	Once the excitation reaches the base of the septum it sweeps upwards, through the ventricle walls causing them to contract (ventricular systole)
9. Gas exchange and smoking
Functions carried out by the human gas exchange system
1.	Clean and warm the air that enter during breathing
2.	Maximise the surface are for diffusion of oxygen and carbon dioxide between the blood and atmosphere
3.	Minimise the distance for this diffusion
4.	Maintain adequate gradients for this diffusion


The lungs are in the thoracic cavity surrounded by pleural membrane that enclose an airtight space. The pleura act to lubricate the lungs to provide friction free movement as the lungs are ventilated by the movement of the diaphragm and ribs
Leading from the throat to the lungs is the trachea. At the base of the trachea are two bronchi, which subdivide extensively forming bronchioles. Bronchioles divide to form even narrower respiratory bronchioles which supply alveoli with air. Cartilage in the trachea and bronchi prevent airways from collapsing due to the changes in pressure caused by breathing.
Trachea: C-shaped cartilage, goblet cells, smooth muscle, cilia
Bronchi: ring cartilage, goblet cells, smooth muscle, cilia
Bronchiole: smooth muscle, cilia
Alveoli: site of gas exchange

Warming and cleaning the air
1.	As air enters, it is warmed to body temperature, and moistened by evaporation to protect delicate surfaces from desiccation
2.	Particles larger than 5-10 micrometres are trapped in nasal hairs and trapped in mucus lining nasal passage
3.	In trachea and bronchi, mucus is produced by goblet cells of the ciliated epithelium. Each goblet cell is swollen with mucin droplets which have been secreted by the cell
4.	Respiratory macrophages are present to destroy any antigenic particles in lining
Alveoli – Structure and function
1.	Alveolar walls contain elastic fibres which stretch and recoil during breathing
2.	Alveoli have one cell thick squamous epithelial wall. Pressed closely against alveoli wall are a network of capillaries with one cell thick endothelial wall  (Gas diffuses quickly through short distances)
3.	Breathing constantly replaces expired air with inspired air. Blood in capillaries is constantly being replaced with deoxygenated blood from heart, and oxygenated blood is carried away. (this maintains the concentration gradient for the gases to diffuse)
Tobacco smoke
Main components: Tar (contains carcinogens), carbon monoxide, and nicotine
Chronic Obstructive Pulmonary Diseases (COPD)
Chronic Bronchitis
1.	Tar in cigarette smoke stimulates goblet cells and mucus glands to enlarge and secrete more mucus
2.	Tar inhibits the cleaning action of ciliated epithelium by destroying cilia
3.	Mucus accumulates in bronchioles
4.	Bacteria, viruses, and dirt begin to accumulate in mucus
5.	Damaged epithelia are replaced with scar tissue
6.	Smooth muscles surrounding becomes thicker narrowing air passage


Emphysema
1.	Phagocytes release enzyme that destroys elastin in alveoli in order to reach infected site in lungs
2.	Elastin is responsible for the recoil of the alveoli during expiration
3.	In absence of elastin, alveoli cannot efficiently stretch and recoil
4.	Bronchioles collapse during expiration, trapping air inside alveoli, which often burst
5.	Large spaces appear in absence of alveoli, reducing surface area of gas exchange system
Lung cancer
1.	Tar in tobacco smoke is carcinogenic
2.	Cause mutations in epithelial cells, which leads to tumour formation (see mitotic cell cycle)
3.	As the cancer develops, it spreads through the bronchial epithelium and enters lymphatic tissue
4.	Cells may break away and form secondary growths (metastasises)
Nicotine
1.	Absorbed readily into blood
2.	Stimulates the nervous system to reduce the diameter of arterioles and release the hormone adrenaline from adrenal glands
3.	Heart rate and blood pressure increase, with reduced blood supply to extremities
4.	Increases damage to arteriole lining resulting in plaque formation (atherosclerosis)
5.	Increases the risk of blood clotting (thrombosis)
Carbon monoxide
1.	Diffuses into RBC and binds permanently to haemoglobin form carboxyhaemoglobin
2.	Reduces the amount of oxygen transported by blood
10. Infectious disease
Diseases is a physiological or psychological, illness or disorder that leads to poor health; associated to a particular set of signs and symptoms and may or may not be communicable
Cholera:
1.	Pathogen: Vibrio cholerae
2.	Method of transmission: food-borne, water-borne
3.	Site of action of pathogen: wall of small intestine (secrets choleragen toxin, that disrupts function of epithelial lining of intestines causing salts and water to leave the blood)
4.	Clinical features: Severe diarrhoea, loss of water and salts, dehydration, weakness
Transmission of cholera
1.	People do not have access to proper sanitation and uncontaminated food
2.	Infected people who are symptomless carriers contaminate water supply, or handle food or cooking utensils without washing their hands
3.	Eating poorly prepared contaminated seafood


Treating cholera
1.	Salts and glucose are given intravenously
2.	If people can drink, the they are given oral rehydration therapy
Preventing cholera
1.	Development of  sewage and water treatment systems
2.	Do not use human sewage in irrigation of vegetables
Malaria:
1.	Pathogen: Plasmodium falciparum, P.vivax,, P.oval, P.malariae
2.	Method of transmission: insect vector (female anopheles mosquito)
3.	Site of action of pathogen: liver, red blood cells, brain
4.	Clinical features: fever, anaemia, nausea, headaches, muscle pains, shivering, sweating, enlarged spleen
Transmission of malaria
1.	Female anopheles mosquito feed on human blood
2.	If person is infected with plasmodium, mosquito will take up gametes in blood meal
3.	Male and female gametes fuse in the mosquitos gut and develop to infective stages which move to mosquitos salivary glands
4.	The infective stages pass from the mosquito to an uninfected person through mosquito saliva
5.	Plasmodium can also cross across the placenta from mother to foetus
Treating malaria
1.	Anti-malarial drugs used for treatment and as prophylactic drugs
2.	Drugs prescribed must be changed if strain becomes resistant to currently prescribed drug
Preventing malaria
1.	 Reduce the number of mosquitos (Biological control measures)
a.	Stocking permanent bodies of water (ponds, irrigation, ditches) with fish that feed on mosquito larvae
b.	Spraying a preparation containing bacillus thuringinesis, which kills mosquito larvae but is not toxic to other forms of life
2.	Avoid being bitten by mosquitos
a.	Sleep beneath mosquito nets
b.	Soaking mosquito nets in insecticide
3.	Use drugs to prevent parasite from infecting people
Worldwide control of malaria
Was not successful for two reason:
1.	Plasmodium became resistant to the drugs used to control it
2.	Mosquitos became resistant to DDT and other insecticides that were used at the time


Worldwide concern over malaria because:
1.	An increase in drug resistant forms of plasmodium
2.	An increase in the proportion of cases caused by P.falciparum (severe malaria)
3.	Difficulty in developing vaccine against malaria
4.	Increasing number of epidemics due to climate change
Factors that may lead to improvement of control of malaria:
1.	Use of modern techniques in gene sequencing and drug design
2.	Development of vaccines targeting different stages of pathogens life cycle
3.	Renewed international will to remove burden of disease in poor parts of the world
Acquired Immune deficiency syndrome (AIDS)
1.	Pathogen: human immunodeficiency virus
2.	Method of transmission: in semen and vaginal fluids during sexual intercourse, infected blood or blood products, contaminated hypodermic syringes, mother to foetus across placenta, at birth, mother to infant in breast milk
3.	Site of action of pathogen: T helper lymphocytes, macrophages, brain cells
4.	Clinical features:
a.	HIV infection- flu-like symptoms and then symptomless
b.	AIDS- opportunistic infections including; pneumonia, TB, and cancers; weight loss, diarrhoea, fever, sweating, dementia

Treating HIV/AIDS

1.	No as of yet known cure
2.	Drug therapy can slow down onset
3.	Drugs are expensive and have a variety of side-effects
4.	Drugs are similar to DNA nucleotides and act in order to stop viral replication

Preventing HIV/AIDS

1.	People are educated about infection to stop spread
2.	Use of condoms, femidoms, and dental dams during sexual intercourse
3.	Contact tracing to identify others who might be HIV+ and control disease spread
4.	Needle exchange schemes to stop spread of disease among drug users
5.	Blood collected from blood donors is heat treated to destroy any virus present
6.	Woman are encouraged not to breast feed to prevent transmission from mother to infant if she is HIV+









Tuberculosis (TB)

1.	Pathogen: Mycobacterium tuberculosis, m.bovis
2.	Method of transmission: airborne droplets (m.tuberculosis), via unpasteurised milk and undercooked meat (m.bovis)
3.	Site of action of pathogen: primary infection in lungs; secondary infection in lymph bode, bones and gut
4.	Clinical features: racking cough, coughing blood, chest pain, shortness of breath. Fever, sweating, weight loss

Transmission of TB
Increase of incidence in TB worldwide due to:
1.	Drug resistant strains of TB
2.	HIV/AIDS pandemic
3.	Poor housing in inner cities and homelessness
4.	Breakdown of TB control programmes

Treating TB

If TB is confirmed:
1.	Patient is isolated at most infective stage (particularly if drug resistant strain)
2.	Treatment involves using several drugs  to ensure all the bacteria is killed
3.	People who do not complete the course of antibiotics harbour drug resistant bacteria which they can then spread to others

Preventing TB

1.	Contact tracing
2.	BCG vaccine use to prevent children from getting disease
3.	Cattle are routinely tested for TB and any found to be infected are destroyed

Measles

1.	Pathogen: Morbillivirus
2.	Method of transmission: droplet infection (highly contagious)
3.	Site of action of pathogen: upper respiratory tract
4.	Clinical features: rash, runny nose, cough, conjunctivitis
5.	Treatment: bed rest and taking medicine to lower the fever

Difficulty of eradicating measles

1.	One-dose-vaccination programme has not been effective due to poor response. Children require several boosters to develop full immunity
2.	Requires a very high percentage coverage to achieve herd immunity >90%
3.	Vaccine is not thermostable


Antibiotics are a type of antimicrobial drug that used to destroy microorganisms or inhibit their growth by interfering with some aspect of cell growth or cell metabolism

Penicillin

1.	Penicillin prevents the formation of cross-links between peptidoglycan polymers in the cell walls of bacteria by inhibiting enzymes that build cross links
2.	Bacterial cell secretes autolysins which make holes in the cell wall
3.	Holes allow walls to stretch so new polypeptide chains can link together
4.	Penicillin prevents cross links from forming
5.	Cell wall becomes progressively weaker
6.	Water enters cell by osmosis causing cell to burst

Antibiotic resistance is when a strain of bacteria is no longer sensitive to an antibiotic, either achieved through horizontal transmission (resistance passed to daughter cells during binary fission) or vertical transmission (passed from one species of bacteria through another through conjugation) through plasmids containing genes providing resistance

Immunity

An antigen is a substance that is foreign to the body and stimulates and immune response

An antibody is a glycoprotein (immunoglobulin) made by plasma cells derived from B-lymphocytes, secreted in response to an antigen; the variable region of the antibody molecule is complimentary in shape to its specific antigen

The immune response is the complex series of responses of the body to the entry of a foreign antigen; it involves the activity of lymphocytes and phagocytes

Non-self refers to any substance or cell that is recognised by the immune system as being foreign and will stimulate an immune response

Self refers to substances produced by the body that the immune system does not recognise as foreign; so immune system is not stimulated

Phagocytes are white blood cells that protect the body by ingesting foreign, potentially harmful particles (phagocytosis)

Neutrophils are a kind of phagocyte that travel through the walls of capillaries and ‘patrol tissue’
During an infection neutrophils are released in large numbers from their stores, but they-are short lived cells

Macrophages are a kind of phagocyte that are larger than neutrophils and tend to be found in organs (lungs, liver, lymph, kidney, spleen). After they are made in the bone marrow, they travel in the blood as monocytes, which mature into macrophages once they settle in the organs.
Are long lived cells and play a crucial role in initiating an immune response by becoming antigen presenting cells (APCs)

Phagocytosis

1.	If pathogens invade the body and cause an infection, some of the cells release histamine
2.	Histamines and antigens released by pathogens attract neutrophils to site of infection
3.	Neutrophils move towards the pathogen which may be clustered together and covered in antibodies
4.	The antibodies further stimulate neutrophils to attack the pathogens
5.	When neutrophil attach to pathogen, the cell surface membrane engulfs the pathogen and traps it within a phagocytic vacuole (endocytosis)
6.	Digestive enzymes are secreted into the vacuole and the pathogen is destroyed

Lymphocytes

B-lymphocyte remains in the bone marrow until they are mature and then spread throughout the body, concentrating in the lymph nodes and spleen

Primary immune response
1.	When an antigen enters the body for the first time (antigen presentation)
2.	Small number of B-lymphocytes in blood with antibody receptor complimentary to antigen bind to antigen and take part in immune response (clonal selection)
3.	Selected B cells divide by mitosis. Some of the daughter cells divide into plasma cells, and others develop into memory cells
4.	Plasma cells secrete antibodies against target antigen to be neutralised
Secondary immune response
5.	The antigen re-enters the body
6.	Memory cells produced in primary response, respond to produce a larger number of plasma cells and memory cells
7.	The response is much faster and a greater concentration of antibodies is produced, thereby suppressing the infection

Immunological memory- refers to the ability of the immune system to respond more rapidly and effectively to a pathogen that has been encountered previously

Antibody is a globular glycoproteins consisting of four polypeptide chains (two heavy chains and two light chains). Disulphide bonds hold the chains together. Each molecule has two identical antigen binding sites which are formed by both light and heavy chains. The antigen binding sites form the variable region which is different on each type of antibody molecule. The hinge region gives the flexibility for the antibody molecule to bind around the antigen

Mechanisms of antibody action:
1.	Combine with antigen preventing it from entering cell
2.	Attach to flagella of bacteria reducing their activity
3.	Agglutination of bacteria preventing spread
4.	Punch holes in bacterial cell walls
5.	Coat bacteria increasing ease of phagocytosis
6.	Combine and neutralise antigens


T-lymphocytes leave the bone marrow, and collect in the thymus where they mature. T-lymphocytes have t-cell receptors that are specific to an antigen, and are activated if the antigen is encountered on one of the host cells.

1.	Antigen enters the body
2.	Macrophage engulfs antigen and displays antigen on its cell surface membrane becoming an antigen presenting cell (APC)
3.	T-lymphocytes with T-receptor complimentary to the antigen, bind to the antigen on an APC and are activated
Helper T cells
4.	Helper T cells divide by mitosis to form helper T cells and memory cells
5.	T helper cells secrete cytokines that;
a.	Stimulate appropriate B cells to divide, develop into plasma cells and secret antibodies
b.	Stimulate macrophages to carry out phagocytosis more vigorously
Killer T cells
4.	Killer T cells divides by mitosis to form killer T cells and memory cells
5.	T cells recognise the antigen, attach themselves to the surface of infected cells, and secret toxic substances (hydrogen peroxide), killing the body cell and the pathogen inside it

Active immunity is immunity gained wen an antigen enters the body, an immune response occurs and antibodies are produced by plasma cells

Passive immunity is immunity gained without an immune response; antibodies against pathogen are introduced into the body instead

Natural immunity is immunity gained by being infected or by receiving from the mother across the placenta or through breast milk

Passive immunity is immunity gained either by vaccination or by injecting antibodies

Vaccination is giving a vaccine containing antigens for a disease, either by injection or by mouth; vaccination confers artificial active immunity

Problems with Vaccines

1.	Poor response as a result of weak immune system, or malnutrition
2.	Live virus may be passed out in faces during primary response and capable of spreading (solution is Herd immunity, where a large number of people are vaccinated at the same time, interrupting transmission in a population so that those who haven’t received vaccine are also protected
3.	Antigenic variation occurs when a pathogenic strain mutates regularly (virus) resulting in antigenic drift (which could lead to antigenic shift), as a result vaccine is no longer effective. Pathogen cannot be targeted as it does not have a stable antigen to develop vaccine against
4.	Antigenic concealment is when pathogens evade attack by the immune system by living inside host cells/ using host cells to evade detection


How the eradication programme of smallpox succeeded

1.	Variola virus was stable; it did not mutate and change its surface antigens, so same vaccine can be used throughout campaign so therefore it was cheap to produce in bulk
2.	The vaccine was made from a harmless strain of a similar virus so it was more effective as virus was ‘live’
3.	The vaccine was freeze-dried, and thermostable so could be kept it high temperatures , so could be used in the tropics
4.	Infected people were easy to identify
5.	Vaccine was easy to administer and was even more effective after the development of the stainless-steel reusable needle
6.	Smallpox did not linger in the body after infection (no reservoir for infection)
7.	Virus did not affect animals, made it easier to break the transmission cycle
8.	Teenagers were enthusiastic vaccinators and educators, being especially effective in remote areas

Autoimmune disease is a condition in which the body produces antibodies against self-antigens, leading to the deterioration and sometimes destruction of tissue

Myasthenia Gravis is an autoimmune condition resulting in progressive muscle weakness. Antibodies are secreted that bind to acetylcholine receptors on the cell surface membrane of muscle cells blocking the transmission from the motor neurone

Monoclonal antibodies is the large scale production of a particular antibody using hybridoma cells.

1.	Antigen injected into mouse spleen to stimulate immune response in mouse resulting in plasma cells that produce antibodies against specific antigen
2.	Plasma cells from mouse spleen are collected
3.	Plasma cells are fused with myeloma cells producing hybridoma cells
4.	Hybridoma cells are tested to identify plasma cells that produces specific antibody
5.	Hybridoma cell is isolated and cultured